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Old 10-29-2012, 08:41 AM   #1
JQL
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Default cuffdiff: extract gene info from chr coordinates

Hi,

Cuffdiff output (gene_exp.txt) has chromosome coordinates. What is the quick way to get gene information?

the output has gene names, but some genes don't have gene names. So chromosome coordinates are probably the only way. I didn't think those XLOC IDs are useful for that.
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Old 10-29-2012, 08:51 AM   #2
GenoMax
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If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start
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Old 10-29-2012, 09:18 AM   #3
JQL
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Thank you GenoMax. That works.

Is there a way to do that in batch mode?

Quote:
Originally Posted by GenoMax View Post
If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start
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Old 10-30-2012, 05:35 AM   #4
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Quote:
Originally Posted by JQL View Post

Is there a way to do that in batch mode?
You can do BioMart queries through their API. See more info here: http://www.biomart.org/martservice.html
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